--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ezBAMQC/src/htslib/test/fieldarith.c	Thu Mar 24 17:12:52 2016 -0400
@@ -0,0 +1,72 @@
+/*  test/fieldarith.c -- CIGAR field arithmetic test suite.
+
+    Copyright (C) 2013 Genome Research Ltd.
+
+    Author: John Marshall <jm18@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <stdio.h>
+
+#include "htslib/sam.h"
+
+int ntests = 0;
+int nfailures = 0;
+
+void check(const bam1_t *aln, const char *testname, const char *tag, int value)
+{
+    int32_t refvalue;
+    uint8_t *aux = bam_aux_get(aln, tag);
+    if (!aux) return;
+    ntests++;
+    refvalue = bam_aux2i(aux);
+    if (value != refvalue) {
+        fprintf(stderr, "%s FAIL for %s: computed %d != %d expected\n",
+                testname, bam_get_qname(aln), value, refvalue);
+        nfailures++;
+    }
+}
+
+int main(int argc, char **argv)
+{
+    bam_hdr_t *header;
+    bam1_t *aln = bam_init1();
+    int i;
+
+    for (i = 1; i < argc; i++) {
+        samFile *in = sam_open(argv[i], "r");
+        if (in == NULL) { perror(argv[1]); return 1; }
+
+        header = sam_hdr_read(in);
+        while (sam_read1(in, header, aln) >= 0) {
+            check(aln, "cigar2qlen", "XQ",
+                  bam_cigar2qlen(aln->core.n_cigar, bam_get_cigar(aln)));
+            check(aln, "cigar2rlen", "XR",
+                  bam_cigar2rlen(aln->core.n_cigar, bam_get_cigar(aln)));
+            check(aln, "endpos", "XE", bam_endpos(aln));
+        }
+
+        bam_hdr_destroy(header);
+        sam_close(in);
+    }
+
+    bam_destroy1(aln);
+
+    return (nfailures > 0);
+}